Good day everyone,
I was following the AMBER Advanced Tutorial 20 Metal Ion Modeling Tutorial, the 12-6 Lennard-Jones (LJ) Nonbonded Model. Now my problem arose by using the suggested input for tleap:
source leaprc.ff12SB #Source the ff12SB force fieldloadoff atomic_ions.lib #Load the library for atomic ionsmol = loadpdb 4V2Y_clean_A_2.pdb #Load the PDB fileloadamberparams frcmod.ionslrcm_cm_spce#Load the frcmod file for divalent metal ionsloadamberparams frcmod.ionsjc_spce #Load the frcmod file for monovalent metal ionssolvatebox mol SPCBOX 8 #Solvate the system using SPC water boxloadamberparams frcmod.spce #Load the frcmod file for SPCE wateraddions mol CL 0 #Neutralize the system using Cl- ionssavepdb mol Zn_4V2Y.pdb #Save the pdb filesaveamberparm mol Zn_4V2Y.prmtop Zn_4V2Y.inpcrd #Save the topology and coordiante filesquit #Quit tleap
The interesting part is:If I have a atomic_ions.lib tleap loads it BEFORE it is called by the script. Besides, this loading somehow blocks the loading of frcmod.ionslrcm_cm_spce and the rest of parameters. The immediate consequence is that addions will fail because it cannot recognized CL (or any ion). Now by changing atomic_ions.lib name to atomic_ions.bil prevented this automatic loading but not its manual loading.Manual loading allowed for the successful competition of the script. I reproduced this behavior in OS X 10.10.3 and ubuntu 12.10 with amber14/ambertools15 fully patched. The former was compiled with intel compilers while the latter with gnu.
Well, best regards.
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Received on Mon Jun 01 2015 - 16:30:02 PDT
